chipAlongChrom: Visualize ChIP intensities along the chromosome
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Value Note Author(s) See Also Examples

This function can visualize the array intensities from a ChIP chip experiment for a chromosomal region or the whole chromosome. It's based on the plotAlongChrom function from the package tilingArray, but provides a different visualization.

## S4 method for signature 'ExpressionSet,probeAnno'
plot(x, y, ...)

chipAlongChrom(eSet,  probeAnno, chrom, xlim, ylim, 
 samples = NULL, paletteName = "Set2", colPal = NULL,
 ylab = "Fold change [log]", ipch = 16, ilwd = 3, ilty = 1,
 icex = 3, gff = NULL,
 featureExclude=c("chromosome", "nucleotide_match","insertion"),
 zeroLine = TRUE, sampleLegend = TRUE, sampleLegendPos = "topleft",
 featureLegend = FALSE, maxInterDistance = 200,  coord = NULL,
 highlight, main, ...)

`eSet`	An expression set containing the (normalized) ChIP intensities, e.g. the result objects from functions `preprocess` and `computeRunningMedians`.
`x`	Corresponds to argument `eSet` when calling the S4 method
`probeAnno`	An object of class `probeAnno` holding genomic position, index and gene association of probes on array.
`y`	Corresponds to argument `probeAnno` when calling the S4 method
`chrom`	character; the chromosome to visualize
`xlim`	start and end genomic coordinates on the chromosome to visualize
`ylim`	minimum and maximum probe intensities for the plot, if missing (default) set to `range(exprs(eSet))`
`samples`	numeric; which samples from the `eSet` are to be shown. Default is to show all samples in the `eSet`,
`paletteName`	character; Name of the RColorBrewer palette to use for sample colors. If the number of samples is greater than the palette size, random colors are taken.
`colPal`	vector of colors to use for the sample intensities. This is alternative to the argument `paletteName` for specifying which colors to use.
`ylab`	character; label for the y-axis, passed on to the plotting function as `ylab`
`ipch`	plot character to use
`icex`	character expansion to use for plotting symbol
`ilwd`	line width of plotted data lines
`ilty`	line type of plotted data lines; passed on to `par(lty)`.
`gff`	data frame containing annotation for genomic feature to be used to further annotate the plot.
`featureExclude`	character vector specifying the feature types in the data.frame `gff` that should not be shown in the plot
`zeroLine`	logical; should a dashed horizontal line at y=0 be put into the plot?
`sampleLegend`	logical; should a sample legend be put into the plot?
`sampleLegendPos`	character; where to put the sample legend; one of ‘topleft’ (default), ‘bottomleft’, ‘topright’, or ‘bottomrigth’
`featureLegend`	logical; should a feature legend be put beneath the plot?
`maxInterDistance`	numeric; only used when `itype` is either "r" or "u"; specifies the maximal distance up to which adjacent probe positions should be connected by a line.
`coord`	optional integer of length 2; can be used instead of `xlim` to specify the start and end coordinates of the genomic region to plot
`highlight`	optional list specifying a genomic region to be highlighted in the shown plot
`main`	optional main title for the plot; if not specified: the default is ‘Chromosome coordinate [bp]’
`...`	further parameters passed on to `grid.polyline` and `grid.points`

invisible list of probe positions (element x) and probe levels (element y) in the selected genomic region.

The S4 method is provided as a mere convenience wrapper.

When plotting a new ‘grid’ plot in an active x11 window that already contains a plot, remember to call grid.newpage() before.

Joern Toedling

ExpressionSet-class, probeAnno-class, grid.points, plotAlongChrom in package tilingArray

  ### load data
  ringoExampleDir <- system.file("exData",package="Ringo")
  load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
  load(file.path(ringoExampleDir,"exampleX.rda"))

  ### show a gene that is well represented on this microarray
  plot(exampleX, exProbeAnno, chrom="9",
       xlim=c(34318000,34321000), ylim=c(-2,4), gff=exGFF)

  ### this should give you the same result as:
  chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
                 ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)